rs753420

Variant names:

• chr19-36152793-T-G
• rs753420

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.303 in 212,566 control chromosomes in the GnomAD database, including 10,591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (7066 hom., cov: 32)
  • Exomes 𝑓: 0.33 (3525 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44606 AN: 151976 Hom.: 7052 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.326 AC: 19703 AN: 60472 Hom.: 3525 Cov.: 0 AF XY: 0.324 AC XY: 9807 AN XY: 30266

Gnomad4 AFR exome AF: 0.277

Gnomad4 AMR exome AF: 0.413

Gnomad4 ASJ exome AF: 0.297

Gnomad4 EAS exome AF: 0.659

Gnomad4 SAS exome AF: 0.414

Gnomad4 FIN exome AF: 0.284

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.316

GnomAD4 genome AF: 0.294 AC: 44663 AN: 152094 Hom.: 7066 Cov.: 32 AF XY: 0.296 AC XY: 22007 AN XY: 74342

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.309

Alfa AF: 0.280 Hom.: 10217

Bravo AF: 0.303

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs753420; hg19: chr19-36643695; COSMIC: COSV53084711; COSMIC: COSV53084711;